tx_makeDT_nucFreq | R Documentation |
This function constructs a list of data.tables that contains nucleotide frequency metrics per nucleotide by transcript:
A = Adenine
C = Cytosine
G = Guanine
T = Thymine
N = Undetermined nucleotide
- = Deletion
. = Insert, not read gap between read1 and read2
The function requires the input of a GRangesList object output by the
tx_reads
function, which should contain sequence alignments in the
transcriptomic space, and a gene annotation in GRanges format, as loaded by
the tx_load_bed
function.
tx_makeDT_nucFreq(
x,
geneAnnot,
genome = NULL,
simplify_IUPAC = "splitForceInt",
fullDT = FALSE,
nCores = 1
)
x |
CompressedGRangesList. Genomic Ranges list containing genomic
alignments data by gene. Constructed via the |
geneAnnot |
GRanges. Gene annotation as loaded by |
genome |
list. The full reference genome sequences, as loaded by
|
simplify_IUPAC |
string. Available options are :
|
fullDT |
logical. Set to TRUE if it is desired to output a data.table with all genes and in the same order as 'geneAnnot' object. |
nCores |
integer. Number of cores to run the function with. Multicore capability not available in Windows OS. |
This function allows for usage of multiple cores to reduce processing times in UNIX-like OS.
data.table
M.A. Garcia-Campos
Other makeDT functions:
tx_makeDT_covNucFreq()
,
tx_makeDT_coverage()
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